Right now, you can't, although this is something I'd like to add.
Right now, you can't,
You could use some other terminating character, and have the Arduino recognize that character or the CR as the carriage return.
You could also write your own version of the Serial Monitor window. I did that in C# in less than an hour. Mine can send, or not, the CR/LF combo.
I have noticed that some people assume that a cr/lf will be sent at the end of every message sent from serial monitor.
I didn't see how to do it however.